The mammalian X chromosome constitutes a vital biological and clinical model for genome regulation through formation of facultative heterochromatin, a phenomenon central to normal development and abrogated in cancer. As we earlier hypothesized, an accumulation of stable XIST RNA structurally associates with one X chromosome in females and initiates a complex process of chromosome remodeling. A central issue now becomes: how does XIST RNA "paint" its parent chromosome and lead to the sweeping condensation and permanent repression of the whole chromosome? Our approach allows molecular, biochemical and structural analyses in direct relation to one another, and will be coupled with bioinformatics of genomic sequence organization. Studies include the role of the tumor suppressor, BRCA1, which recent findings link to XIST RNA and maintenance of dosage compensation. Other key questions address the interrelationship of biochemical and structural changes with transcriptional repression, when XIST is expressed in normal embryonic context, and when the developmental or chromosomal context is manipulated. Human genome sequence analysis will be pursued with potential to reveal sequences in "junk" DNA involved in chromosome architecture and XIST RNA binding. The significance of this research extends from elucidating fundamental mechanisms of developmental gene regulation and chromosome structure, to testing innovative hypotheses and approaches with direct clinical implications.